8emw

Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes

Method: ELECTRON MICROSCOPY Dmax: 127.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

Homo sapiens

UniProt Q01970

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 10–1234 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 2 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 2 (P59768) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLCB3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–1232; UniProt 10–1234

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–340 Chain C; UniProt 1–340 Not recorded 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 × 1 (Q01970) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 2 (P59768) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340 Author chain C; PDBConstruct 1–340; UniProt 1–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–68 Chain G; UniProt 1–68 Not recorded 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 × 1 (Q01970) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 2 (P62873) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 3–70; UniProt 1–68 Author chain G; PDBConstruct 3–70; UniProt 1–68

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8emw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8emw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8emw
Deposition date deposition_date2022-09-28
Structure title titlePhospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
Keywords keywordsPIP2 degradation, IP3 production, DAG production, G protein signaling, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.72
Radius of gyration Rg (electron density) rg_electron41.21
Forward intensity I(0) i0425846000.00
Molecular weight molecular_weight166920.0 kDa
Excluded volume excluded_volume208030 ų
Envelope volume envelope_volume285170 ų
Hydration-shell volume shell_volume57852 ų
Envelope diameter envelope_diameter131.6
Shell Rg shell_rg46.47
Envelope Rg envelope_rg40.73
Shape Rg shape_rg41.19
Total Rg total_rg41.56
Total atoms total_atoms11714
Residues n_residues1506
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.4
Rg (real space) rg_real41.64
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real4.2580e+08
I(0) uncertainty (real space) i0_real_error6.7550e+06
Rg (reciprocal space) rg_reciprocal41.72
I(0) (reciprocal space) i0_reciprocal425900000.0000
Solution quality estimate total_estimate0.8832
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.3
Skewness Skewness skewness0.129
Kurtosis Kurtosis kurtosis-0.785
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha128500000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.595

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id8emwA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id8emwB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8emwC01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)